It sounds like a lot of your files don't have tags in them. If the file names and/or directory names have the information, you can probably use this tool to help:
Tools > Library Tools > Fill properties from filename
You may have to design your own template, but that's not too hard. The preview shows you what tags it is going to change before you press OK. You may need to do this in groups of files that are laid out in a similar way, or do multiple passes.
In the future, you should consider doing your disk reorganization using JRiver's built in tool: Rename, Move, and Copy files. It's designed to do these kinds of moves and help you maintain a very organized setup on disk. Good luck!
Brian.